Dynamic report for checking simulation design (4.5)

True mean Progression Free Time (PFT)

     Enzalutamide Abiraterone Carboplatin Cabazitaxel Docetaxel
----         7.11        7.11       13.75        7.11      7.11
---+         7.11        7.11       13.75        7.11      7.11
--+-         7.11        7.11       13.75        7.11      7.11
--++         7.11        7.11       13.75        7.11      7.11
-+--         7.11        7.11       13.75        7.11      7.11
-+-+         7.11        7.11       13.75        7.11      7.11
-++-         7.11        7.11       13.75        7.11      7.11
-+++         7.11        7.11       13.75        7.11      7.11
+---         7.11        7.11       13.75        7.11      7.11
+--+         7.11        7.11       13.75        7.11      7.11
+-+-         7.11        7.11       13.75        7.11      7.11
+-++         7.11        7.11       13.75        7.11      7.11
++--         7.11        7.11       13.75        7.11      7.11
++-+         7.11        7.11       13.75        7.11      7.11
+++-         7.11        7.11       13.75        7.11      7.11


Graduation output

$superiority
            Enzalutamide Abiraterone Carboplatin Cabazitaxel Docetaxel
all                    0           0           1           0         0
TP53- & AR-            0           0           0           0         0
TP53+                  0           0           1           0         0
DRD+                   0           0           0           0         0
TEfus+                 0           0           0           0         0

$inferiority
            Enzalutamide Abiraterone Carboplatin Cabazitaxel Docetaxel
all                    0           0           0           0         0
TP53- & AR-            0           0           0           0         0
TP53+                  0           0           0           0         0
DRD+                   0           0           0           0         0
TEfus+                 0           0           0           0         0


Final probability of superioriry by signatures and biomarkers subtypes

$p_sign
            Enzalutamide Abiraterone Carboplatin Cabazitaxel Docetaxel
all                 0.65        0.66        0.99        0.53      0.75
TP53- & AR-         0.41        0.46        1.00        0.87      0.69
TP53+               0.84        0.71        0.94        0.61      0.57
DRD+                0.55        0.72        0.85        0.72      0.69
TEfus+              0.64        0.31        0.91        0.57      0.74

$p_type
     Enzalutamide Abiraterone Carboplatin Cabazitaxel Docetaxel
----         0.21        0.31        1.00        0.15      0.45
---+         0.73        0.65        0.93        0.80      0.84
--+-         0.97        0.60        0.93        0.24      0.52
--++         0.51        0.62        0.97        0.74      0.53
-+--         0.33        0.34        0.84        0.68      0.45
-+-+         0.46        0.50        0.66        0.87      0.53
-++-         0.48        0.74        0.64        0.54      0.35
-+++         0.68        0.53        0.55        0.50      0.51
+---         0.49        0.71        0.65        0.26      0.46
+--+         0.34        0.09        0.38        0.17      0.54
+-+-         0.53        0.61        0.60        0.55      0.52
+-++         0.57        0.25        0.64        0.31      0.54
++--         0.30        0.70        0.79        0.32      0.71
++-+         0.47        0.45        0.47        0.40      0.64
+++-         0.73        0.70        0.60        0.76      0.66








     Control Enzalutamide Abiraterone Carboplatin Cabazitaxel Docetaxel
----     153           28          59          27          43        43
---+      19           14          15           4          16        10
--+-      54           54          29          16          12        18
--++      38           12          19           6          25        15
-+--      37            1           2           8           8         5
-+-+      17            4           3           9          12         7
-++-       4            2           6           2           3         3
-+++       4            3           0           0           1         3
+---      19            8          15           2           2         7
+--+      11            7           5           1           5        16
+-+-       3            2           4           0           1         1
+-++      19            4           5           3           7        10
++--       5            6           6           2           6         5
++-+       1            1           0           2           2         3
+++-       5            1           1           1           2         1
            Control Enzalutamide Abiraterone Carboplatin Cabazitaxel Docetaxel
all             389          147         169          83         145       147
TP53- & AR-     226           47          79          48          79        65
TP53+           127           78          64          28          51        51
DRD+             73           18          18          24          34        27
TEfus+          109           45          47          25          68        64





Number of events, PT, and rate by subtype (over time)




Number of events, PT, and rate by signature (over time)



Analysis of final simulated results

Sample of 10 rows:

      id         trt         trt2 line subtype delta month0     time_m all TP53- & AR- TP53+ DRD+ TEfus+
565  507 Cabazitaxel  Cabazitaxel    1    +-++     1     16  1.1326152   1           0     1    0      1
264  244     Control    Docetaxel    1    --+-     1      8  4.6989086   1           0     1    0      0
158  150   Docetaxel    Docetaxel    1    +--+     1      4 12.2078841   1           0     0    0      1
120  113 Carboplatin  Carboplatin    1    +++-     1      3  1.6844444   1           0     1    1      0
1005 902     Control Enzalutamide    1    ----     1     30  0.9303245   1           1     0    0      0
261  241     Control Enzalutamide    1    ----     1      8 23.1234898   1           1     0    0      0
1006 903     Control Enzalutamide    1    ----     1     30  2.2252601   1           1     0    0      0
262  242     Control  Abiraterone    1    ----     1      8  5.5241276   1           1     0    0      0
956  866 Cabazitaxel  Cabazitaxel    1    -+-+     1     28  1.0317802   1           1     0    1      1
131  123     Control  Abiraterone    1    --+-     1      4  6.9556186   1           0     1    0      0

Descriptives

Mean number of progressions and follow-up time:

$all
# A tibble: 6 x 4
  trt          progressions    PT   rate
  <fct>               <dbl> <dbl>  <dbl>
1 Control               334 2387. 0.140 
2 Enzalutamide          143 1097. 0.130 
3 Abiraterone           147 1038. 0.142 
4 Carboplatin            78 1030. 0.0757
5 Cabazitaxel           144  962. 0.150 
6 Docetaxel             122  922. 0.132 

$`TP53- & AR-`
# A tibble: 6 x 4
  trt          progressions    PT   rate
  <fct>               <dbl> <dbl>  <dbl>
1 Control               197 1454. 0.136 
2 Enzalutamide           54  347. 0.156 
3 Abiraterone            74  503. 0.147 
4 Carboplatin            44  626. 0.0703
5 Cabazitaxel            76  585. 0.130 
6 Docetaxel              51  398. 0.128 

$`TP53+`
# A tibble: 6 x 4
  trt          progressions    PT   rate
  <fct>               <dbl> <dbl>  <dbl>
1 Control               108  702. 0.154 
2 Enzalutamide           65  595. 0.109 
3 Abiraterone            54  381. 0.142 
4 Carboplatin            27  319. 0.0846
5 Cabazitaxel            50  312. 0.160 
6 Docetaxel              50  315. 0.159 

$`DRD+`
# A tibble: 6 x 4
  trt          progressions    PT   rate
  <fct>               <dbl> <dbl>  <dbl>
1 Control                65  470. 0.138 
2 Enzalutamide           18  112. 0.161 
3 Abiraterone            10  105. 0.0950
4 Carboplatin            24  269. 0.0893
5 Cabazitaxel            26  236. 0.110 
6 Docetaxel              22  181. 0.122 

$`TEfus+`
# A tibble: 6 x 4
  trt          progressions    PT   rate
  <fct>               <dbl> <dbl>  <dbl>
1 Control                89  599. 0.148 
2 Enzalutamide           48  348. 0.138 
3 Abiraterone            45  254. 0.177 
4 Carboplatin            25  297. 0.0843
5 Cabazitaxel            64  478. 0.134 
6 Docetaxel              51  416. 0.123 

Kaplan-Meier results:

$all
Call: survfit(formula = Surv(time_m, delta) ~ trt, data = d)

                   n events median 0.95LCL 0.95UCL
trt=Control      439    334   4.76    4.35    5.73
trt=Enzalutamide 166    143   5.90    5.17    7.19
trt=Abiraterone  181    147   5.33    4.43    6.37
trt=Carboplatin   89     78   9.00    6.19   13.45
trt=Cabazitaxel  164    144   4.74    3.88    5.73
trt=Docetaxel    158    122   5.18    4.56    6.54

$`TP53- & AR-`
Call: survfit(formula = Surv(time_m, delta) ~ trt, data = d)

                   n events median 0.95LCL 0.95UCL
trt=Control      253    197   4.83    4.19    6.55
trt=Enzalutamide  58     54   5.78    3.66    7.94
trt=Abiraterone   85     74   5.26    3.83    6.58
trt=Carboplatin   52     44  10.12    5.65   16.18
trt=Cabazitaxel   91     76   5.73    5.20    7.01
trt=Docetaxel     70     51   4.70    3.88    6.93

$`TP53+`
Call: survfit(formula = Surv(time_m, delta) ~ trt, data = d)

                   n events median 0.95LCL 0.95UCL
trt=Control      144    108   4.42    3.63    5.55
trt=Enzalutamide  83     65   6.86    5.19    9.23
trt=Abiraterone   68     54   5.23    3.86    7.35
trt=Carboplatin   29     27   9.00    6.23   17.01
trt=Cabazitaxel   55     50   4.28    3.17    6.18
trt=Docetaxel     55     50   5.26    3.61    6.85

$`DRD+`
Call: survfit(formula = Surv(time_m, delta) ~ trt, data = d)

                  n events median 0.95LCL 0.95UCL
trt=Control      79     65   5.03    3.27    7.00
trt=Enzalutamide 19     18   4.16    2.22   12.39
trt=Abiraterone  19     10   4.96    4.20      NA
trt=Carboplatin  25     24   6.71    5.63   15.06
trt=Cabazitaxel  36     26   6.74    3.88   13.33
trt=Docetaxel    30     22   6.54    3.88    9.26

$`TEfus+`
Call: survfit(formula = Surv(time_m, delta) ~ trt, data = d)

                   n events median 0.95LCL 0.95UCL
trt=Control      119     89   4.95    3.65    6.41
trt=Enzalutamide  53     48   5.46    4.82    9.40
trt=Abiraterone   51     45   3.48    2.60    5.54
trt=Carboplatin   28     25   7.04    5.49   17.01
trt=Cabazitaxel   77     64   5.18    3.88    6.33
trt=Docetaxel     68     51   5.26    4.56    8.30